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Chromosome interaction copy number analysis of mouse neonatal liver cells, and undifferentiated and differentiated embryonic stem cells using circular chromosome conformation capture (4C) assays


ABSTRACT: Using Circular chromosome conformation capture (4C) assay to uncovers epigenetically regulated intra- and inter-chromosomal interaction network To examine restrictions imposed by the nuclear structure on such cis/trans-chromosomal networks, we developed a high-throughput screening assay 4C and identified 114 different sequences from all autosomes in mouse liver cells. To check the relative frequencies of interactions, the 114 sequences were PCR amplified and spotted on glass to make dedicated microarray. The microarray and 3C validation showed that most of the sequences interact with primarily the maternally inherited H19 imprinting control region (ICR). The epigenetic feature of these interactions was highlighted by the observation that 19% of 4C library sequences are derived from 11 different imprinted domains. In some of these instances, differentially methylated regions (DMRs) interact both in cis and in trans. Moreover, the patterns of chromosomal interactions undergo reprogramming during in vitro maturation of embryonic stem cells. We propose that the nuclear organization of mammalian cells displays considerable plasticity to potentially throw new light on development, cancer epigenetics and evolution of imprinting. Keywords: Chromosome conformation capture, CTCF, ICR(Imprinting Control Region) 4C Assay on MBoI, MSeI, PM-Liv and MM-Liv

ORGANISM(S): Mus musculus

SUBMITTER: Rolf Ohlsson 

PROVIDER: E-GEOD-23788 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

CTCF-binding sites within the H19 ICR differentially regulate local chromatin structures and cis-acting functions.

Guibert Sylvain S   Zhao Zhihu Z   Sjölinder Mikael M   Göndör Anita A   Fernandez Alejandro A   Pant Vinod V   Ohlsson Rolf R  

Epigenetics 20120401 4


It is generally assumed that CTCF-binding sites are synonymous with the demarcation of expression domains by promoting the formation of chromatin loops. We have proposed earlier, however, that such features may be context-dependent. In support of this notion, we show here that chromatin loop structures, impinging on CTCF-binding sites 1/2 and 3/4 at the 5' and 3'-ends, respectively, within the maternal allele of the H19 imprinting control region (ICR), differ significantly. Although abrogation o  ...[more]

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